Construction of an adjacency matrixΒΆ

In this example we create an adjacency matrix of the CA atoms in the lysozyme crystal structure (PDB: 1AKI). The values in the adjacency matrix m are m[i,j] = 1 if distance(i,j) <= threshold else 0.

Adjacency matrix of the lysozyme crystal structure
# Code source: Patrick Kunzmann
# License: BSD 3 clause

from tempfile import gettempdir
import biotite
import biotite.structure as struc
import as strucio
import biotite.database.rcsb as rcsb
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap

file_name = rcsb.fetch("1aki", "mmtf", gettempdir())
array = strucio.load_structure(file_name)
# We only consider CA atoms
ca = array[array.atom_name == "CA"]
# 7 Angstrom adjacency threshold
threshold = 7
# Create cell list of the CA atom array
# for efficient measurement of adjacency
cell_list = struc.CellList(ca, cell_size=threshold)
adjacency_matrix = cell_list.create_adjacency_matrix(threshold)

figure = plt.figure()
ax = figure.add_subplot(111)
cmap = ListedColormap(["white", biotite.colors["dimgreen"]])
ax.matshow(adjacency_matrix, cmap=cmap, origin="lower")
ax.set_xlabel("Residue number")
ax.set_ylabel("Residue number")
ax.set_title("Adjacency matrix of the lysozyme crystal structure")

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